_sample = pd.read_table('meta/sample.tsv', index_col='sample_id') sample.join(_sample[['plate_well', 'source_sample_id']])[sample.has_mgen][['source_sample_id', 'sample_notes', 'plate_well']].to_csv('all_sequenced_samples.csv')
sample_x_sotu.loc[sample.sample_type.isin(['donor_mean', 'baseline'])].groupby(sotu_to_taxonomy.p__, axis='columns').sum().mean().sort_values()
print(recipient[[ 'treatment_abx_pre', 'maintenance_', 'donor_subject_id', 'remission', 'responder', 'withdrawal_due_to_failure', ]].to_markdown())
sample_x_rotu.join(m, how='left').groupby(['subject_id', 'sample_type']).apply(len).unstack()